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Computational Neuroscience

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The vast differences between the brain’s neural circuitry and a computer’s silicon circuitry might suggest that they have nothing in common. In fact, as Dana Ballard argues in this book, computational tools are essential for understanding brain function. Ballard shows that the hierarchical organization of the brain has many parallels with the hierarchical organization of computing; as in silicon computing, the complexities of brain computation can be dramatically simplified when its computation is factored into different levels of abstraction.

Drawing on several decades of progress in computational neuroscience, together with recent results in Bayesian and reinforcement learning methodologies, Ballard factors the brain’s principal computational issues in terms of their natural place in an overall hierarchy. Each of these factors leads to a fresh perspective. A neural level focuses on the basic forebrain functions and shows how processing demands dictate the extensive use of timing-based circuitry and an overall organization of tabular memories. An embodiment level organization works in reverse, making extensive use of multiplexing and on-demand processing to achieve fast parallel computation. An awareness level focuses on the brain’s representations of emotion, attention and consciousness, showing that they can operate with great economy in the context of the neural and embodiment substrates.

The event-related potential (ERP) technique, in which neural responses to specific events are extracted from the EEG, provides a powerful noninvasive tool for exploring the human brain. This volume describes practical methods for ERP research along with the underlying theoretical rationale. It offers researchers and students an essential guide to designing, conducting, and analyzing ERP experiments. This second edition has been completely updated, with additional material, new chapters, and more accessible explanations. Freely available supplementary material, including several online-only chapters, offer expanded or advanced treatment of selected topics.

The first half of the book presents essential background information, describing the origins of ERPs, the nature of ERP components, and the design of ERP experiments. The second half of the book offers a detailed treatment of the main steps involved in conducting ERP experiments, covering such topics as recording the EEG, filtering the EEG and ERP waveforms, and quantifying amplitudes and latencies. Throughout, the emphasis is on rigorous experimental design and relatively simple analyses. New material in the second edition includes entire chapters devoted to components, artifacts, measuring amplitudes and latencies, and statistical analysis; updated coverage of recording technologies; concrete examples of experimental design; and many more figures. Online chapters cover such topics as overlap, localization, writing and reviewing ERP papers, and setting up and running an ERP lab.

Theory and Practice

This book offers a comprehensive guide to the theory and practice of analyzing electrical brain signals. It explains the conceptual, mathematical, and implementational (via Matlab programming) aspects of time-, time-frequency- and synchronization-based analyses of magnetoencephalography (MEG), electroencephalography (EEG), and local field potential (LFP) recordings from humans and nonhuman animals. It is the only book on the topic that covers both the theoretical background and the implementation in language that can be understood by readers without extensive formal training in mathematics, including cognitive scientists, neuroscientists, and psychologists.

Readers who go through the book chapter by chapter and implement the examples in Matlab will develop an understanding of why and how analyses are performed, how to interpret results, what the methodological issues are, and how to perform single-subject-level and group-level analyses. Researchers who are familiar with using automated programs to perform advanced analyses will learn what happens when they click the “analyze now” button.

The book provides sample data and downloadable Matlab code. Each of the 38 chapters covers one analysis topic, and these topics progress from simple to advanced. Most chapters conclude with exercises that further develop the material covered in the chapter. Many of the methods presented (including convolution, the Fourier transform, and Euler’s formula) are fundamental and form the groundwork for other advanced data analysis methods. Readers who master the methods in the book will be well prepared to learn other approaches.

Computational and Mathematical Modeling of Neural Systems

Theoretical neuroscience provides a quantitative basis for describing what nervous systems do, determining how they function, and uncovering the general principles by which they operate. This text introduces the basic mathematical and computational methods of theoretical neuroscience and presents applications in a variety of areas including vision, sensory-motor integration, development, learning, and memory.

The book is divided into three parts. Part I discusses the relationship between sensory stimuli and neural responses, focusing on the representation of information by the spiking activity of neurons. Part II discusses the modeling of neurons and neural circuits on the basis of cellular and synaptic biophysics. Part III analyzes the role of plasticity in development and learning. An appendix covers the mathematical methods used, and exercises are available on the book's Web site.

From Laboratory to Theory

Vision is one of the most active areas in biomedical research, and visual psychophysical techniques are a foundational methodology for this research enterprise. Visual psychophysics, which studies the relationship between the physical world and human behavior, is a classical field of study that has widespread applications in modern vision science. Bridging the gap between theory and practice, this textbook provides a comprehensive treatment of visual psychophysics, teaching not only basic techniques but also sophisticated data analysis methodologies and theoretical approaches. It begins with practical information about setting up a vision lab and goes on to discuss the creation, manipulation, and display of visual images; timing and integration of displays with measurements of brain activities and other relevant techniques; experimental designs; estimation of behavioral functions; and examples of psychophysics in applied and clinical settings.

The book's treatment of experimental designs presents the most commonly used psychophysical paradigms, theory-driven psychophysical experiments, and the analysis of these procedures in a signal-detection theory framework. The book discusses the theoretical underpinnings of data analysis and scientific interpretation, presenting data analysis techniques that include model fitting, model comparison, and a general framework for optimized adaptive testing methods. It includes many sample programs in Matlab with functions from Psychtoolbox, a free toolbox for real-time experimental control. Once students and researchers have mastered the material in this book, they will have the skills to apply visual psychophysics to cutting-edge vision science.

Crucial to understanding how the brain works is connectivity, and the centerpiece of brain connectivity is the connectome, a comprehensive description of how neurons and brain regions are connected. The human brain is a network of extraordinary complexity—a network not by way of metaphor, but in a precise and mathematical sense: an intricate web of billions of neurons connected by trillions of synapses. How this network is connected is important for virtually all facets of the brain’s integrative function. In this book, Olaf Sporns surveys current efforts to chart these connections—to map the human connectome.

Sporns, a pioneer in the field who was the first to define and use the term "connectome," argues that the nascent field of connectomics has already begun to influence the way many neuroscientists collect, analyze, and think about their data. Moreover, the idea of mapping the connections of the human brain in their entirety has captured the imaginations of researchers across several disciplines including human cognition, brain and mental disorders, and complex systems and networks. Sporns describes the biological and conceptual foundations of the connectome; the many research challenges it faces; the many cutting-edge empirical strategies, from electron microscopy to magnetic resonance imaging, deployed to map brain connectivity; the relationship between structure and function; and the wide array of network computational approaches to connectomics. Discovering the Human Connectome offers the first comprehensive overview of current empirical and computational approaches in this rapidly developing field.

Global State Interactions

The consideration of time or dynamics is fundamental for all aspects of mental activity--perception, cognition, and emotion--because the main feature of brain activity is the continuous change of the underlying brain states even in a constant environment. The application of nonlinear dynamics to the study of brain activity began to flourish in the 1990s when combined with empirical observations from modern morphological and physiological observations. This book offers perspectives on brain dynamics that draw on the latest advances in research in the field. It includes contributions from both theoreticians and experimentalists, offering an eclectic treatment of fundamental issues.

Topics addressed range from experimental and computational approaches to transient brain dynamics to the free-energy principle as a global brain theory. The book concludes with a short but rigorous guide to modern nonlinear dynamics and their application to neural dynamics.

The Emerging Intersection between Control Theory and Neuroscience

Over the past sixty years, powerful methods of model-based control engineering have been responsible for such dramatic advances in engineering systems as autolanding aircraft, autonomous vehicles, and even weather forecasting. Over those same decades, our models of the nervous system have evolved from single-cell membranes to neuronal networks to large-scale models of the human brain. Yet until recently control theory was completely inapplicable to the types of nonlinear models being developed in neuroscience. The revolution in nonlinear control engineering in the late 1990s has made the intersection of control theory and neuroscience possible. In Neural Control Engineering, Steven Schiff seeks to bridge the two fields, examining the application of new methods in nonlinear control engineering to neuroscience. After presenting extensive material on formulating computational neuroscience models in a control environment—including some fundamentals of the algorithms helpful in crossing the divide from intuition to effective application—Schiff examines a range of applications, including brain-machine interfaces and neural stimulation. He reports on research that he and his colleagues have undertaken showing that nonlinear control theory methods can be applied to models of single cells, small neuronal networks, and large-scale networks in disease states of Parkinson’s disease and epilepsy. With Neural Control Engineering the reader acquires a working knowledge of the fundamentals of control theory and computational neuroscience sufficient not only to understand the literature in this trandisciplinary area but also to begin working to advance the field. The book will serve as an essential guide for scientists in either biology or engineering and for physicians who wish to gain expertise in these areas.

A Laboratory Study of Multimodal Semiotic Interaction in the Age of Computers

The results of fMRI brain scanning require extensive analysis in the laboratory. In Handling Digital Brains, Morana Alač shows that fMRI researchers do not sit passively staring at computer screens but actively involve their bodies in laboratory practice. Discussing fMRI visuals with colleagues, scientists animate the scans with gestures, and talk as they work with computers. Alač argues that to understand how digital scientific visuals take on meaning we must consider their dynamic coordination with gesture, speech, and working hands. These multimodal actions, she suggests, are an essential component of digital scientific visuals.

A semiotician trained in cognitive science, Alač grounds her discussion in concepts from Peirce's semiotics and her methodology in ethnography and multimodal conversation analysis. Basing her observations on videotaped records of activity in three fMRI research labs, Alač describes scientists' manual engagement with digital visuals of the human brain. Doing so, she turns her attention to the issue of practical thinking. Alač argues that although fMRI technology directs scientists to consider human thinking in terms of an individual brain, scientific practices in the fMRI lab demonstrate thinking that engages the whole lived body and the world in which the body is situated. The turn toward the digital does not bring with it abstraction but a manual and embodied engagement. The practical and multimodal engagement with digital brains in the laboratory challenges certain assumptions behind fMRI technology; it suggests our hands are essential to learning, and the making of meaning.

Functional magnetic resonance imaging (fMRI), which allows researchers to observe neural activity in the human brain noninvasively, has revolutionized the scientific study of the mind. An fMRI experiment produces massive amounts of highly complex data; researchers face significant challenges in analyzing the data they collect. This book offers an overview of the most widely used statistical methods of analyzing fMRI data. Every step is covered, from preprocessing to advanced methods for assessing functional connectivity. The goal is not to describe which buttons to push in the popular software packages but to help readers understand the basic underlying logic, the assumptions, the strengths and weaknesses, and the appropriateness of each method.

The book covers all of the important current topics in fMRI data analysis, including the relation of the fMRI BOLD (blood oxygen-level dependent) response to neural activation; basic analyses done in virtually every fMRI article—preprocessing, constructing statistical parametrical maps using the general linear model, solving the multiple comparison problem, and group analyses; the most popular methods for assessing functional connectivity—coherence analysis and Granger causality; two widely used multivariate approaches, principal components analysis and independent component analysis; and a brief survey of other current fMRI methods. The necessary mathematics is explained at a conceptual level, but in enough detail to allow mathematically sophisticated readers to gain more than a purely conceptual understanding. The book also includes short examples of Matlab code that implement many of the methods described; an appendix offers an introduction to basic Matlab matrix algebra commands (as well as a tutorial on matrix algebra). A second appendix introduces multivariate probability distributions.

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